7JUX

Crystal Structure of KSR1:MEK1 in complex with AMP-PNP, and allosteric MEK inhibitor Trametinib


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.34 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.265 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Structural basis for the action of the drug trametinib at KSR-bound MEK.

Khan, Z.M.Real, A.M.Marsiglia, W.M.Chow, A.Duffy, M.E.Yerabolu, J.R.Scopton, A.P.Dar, A.C.

(2020) Nature 588: 509-514

  • DOI: 10.1038/s41586-020-2760-4
  • Primary Citation of Related Structures:  
    7JUQ, 7JUR, 7JUS, 7JUT, 7JUU, 7JUV, 7JUW, 7JUX, 7JUY, 7JUZ, 7JV0, 7JV1

  • PubMed Abstract: 
  • The MAPK/ERK kinase MEK is a shared effector of the frequent cancer drivers KRAS and BRAF that has long been pursued as a drug target in oncology 1 , and more recently in immunotherapy 2,3 and ageing 4 . However, many MEK inhibitors are limited owing to on-target toxicities 5-7 and drug resistance 8-10 ...

    The MAPK/ERK kinase MEK is a shared effector of the frequent cancer drivers KRAS and BRAF that has long been pursued as a drug target in oncology 1 , and more recently in immunotherapy 2,3 and ageing 4 . However, many MEK inhibitors are limited owing to on-target toxicities 5-7 and drug resistance 8-10 . Accordingly, a molecular understanding of the structure and function of MEK within physiological complexes could provide a template for the design of safer and more effective therapies. Here we report X-ray crystal structures of MEK bound to the scaffold KSR (kinase suppressor of RAS) with various MEK inhibitors, including the clinical drug trametinib. The structures reveal an unexpected mode of binding in which trametinib directly engages KSR at the MEK interface. In the bound complex, KSR remodels the prototypical allosteric pocket of the MEK inhibitor, thereby affecting binding and kinetics, including the drug-residence time. Moreover, trametinib binds KSR-MEK but disrupts the related RAF-MEK complex through a mechanism that exploits evolutionarily conserved interface residues that distinguish these sub-complexes. On the basis of these insights, we created trametiglue, which limits adaptive resistance to MEK inhibition by enhancing interfacial binding. Our results reveal the plasticity of an interface pocket within MEK sub-complexes and have implications for the design of next-generation drugs that target the RAS pathway.


    Organizational Affiliation

    Department of Pharmacological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA. arvin.dar@mssm.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Kinase suppressor of Ras 1A334Homo sapiensMutation(s): 0 
Gene Names: KSR1KSR
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IVT5 (Homo sapiens)
Explore Q8IVT5 
Go to UniProtKB:  Q8IVT5
PHAROS:  Q8IVT5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IVT5
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Dual specificity mitogen-activated protein kinase kinase 1B [auth C]384Oryctolagus cuniculusMutation(s): 0 
Gene Names: MAP2K1MEK1PRKMK1
EC: 2.7.12.2
UniProt
Find proteins for P29678 (Oryctolagus cuniculus)
Explore P29678 
Go to UniProtKB:  P29678
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29678
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QOM (Subject of Investigation/LOI)
Query on QOM

Download Ideal Coordinates CCD File 
F [auth C]Trametinib
C26 H23 F I N5 O4
LIRYPHYGHXZJBZ-UHFFFAOYSA-N
 Ligand Interaction
ANP (Subject of Investigation/LOI)
Query on ANP

Download Ideal Coordinates CCD File 
C [auth A],
E [auth C]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.34 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.265 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.47α = 90
b = 137.47β = 90
c = 221.8γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)United States5R01CA227636-02
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)United States1DP2CA186570-01

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 2.0: 2020-10-07
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2020-12-30
    Changes: Database references